There is now direct flights from JB to Tawau, but only 1 timing a day. Promo price now is as low as RM79/way.
It depends on where u want to stay, if it's gonna be at semporna, then it doesnt really matter what time you arrive, coz they will arrange for transport for you from tawau to semporna, u wont be able to dive on that day, but it kinda saves alot of hassle for u having to transit, and with the promo price, it saves u a bomb!
Scuba Junkie is quite ok, u can dive from Semporna first, and the day before u dive Sipadan, u will move over to their Mabul resort.